|
| Status |
Public on Mar 07, 2024 |
| Title |
DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr ICRF-193 R2 |
| Sample type |
SRA |
| |
|
| Source name |
uterine/cervical adenocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa-S3 (CCL-2.2)
tissue: uterine/cervical adenocarcinoma cell line
|
| Treatment protocol |
Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t3hr, and cells were fixed at t8hr. G1 cells were isolated by FACS.
|
| Growth protocol |
HeLa-S3 cells were cultured in glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for separate replicates and combined replicates.
Assembly: hg38
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Job Dekker |
| E-mail(s) |
job.dekker@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School/HHMI
|
| Department |
Program in Systems Biology
|
| Lab |
Dekker Lab
|
| Street address |
368 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01606 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE198610 |
Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis |
|
| Relations |
| BioSample |
SAMN26660512 |
| SRA |
SRX14464196 |
